4AYC Ligase date Jun 20, 2012
title Rnf8 Ring Domain Structure
authors F.Mattiroli, J.H.A.Vissers, W.J.Van Dijk, P.Ikpa, E.Citterio, W.V J.A.Marteijn, T.K.Sixma
compound source
Molecule: E3 Ubiquitin-Protein Ligase Rnf8
Chain: A
Fragment: Ring Domain, Residues 351-485
Synonym: Ring Finger Protein 8
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Plyss
Expression_system_vector_type: Plasmid
Expression_system_vector: Pgex6p

Molecule: E3 Ubiquitin-Protein Ligase Rnf8
Chain: B
Fragment: Ring Domain, Residues 351-485
Synonym: Ring Finger Protein 8
Ec: 6.3.2.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Plyss
Expression_system_vector_type: Plasmid
Expression_system_vector: Pgex6p
symmetry Space Group: P 21 21 2
R_factor 0.19973 R_Free 0.22948
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.374 213.717 34.102 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand CL, CPQ, CSO, GOL, SO4, ZN enzyme Ligase E.C.6.3.2 BRENDA
Primary referenceRNF168 Ubiquitinates K13-15 on H2A/H2AX to Drive DNA Damage Signaling., Mattiroli F, Vissers JH, van Dijk WJ, Ikpa P, Citterio E, Vermeulen W, Marteijn JA, Sixma TK, Cell. 2012 Sep 14;150(6):1182-95. doi: 10.1016/j.cell.2012.08.005. PMID:22980979
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (103 Kb) [Save to disk]
  • Biological Unit Coordinates (4ayc.pdb1.gz) 193 Kb
  • LPC: Ligand-Protein Contacts for 4AYC
  • CSU: Contacts of Structural Units for 4AYC
  • Structure Factors (382 Kb)
  • Retrieve 4AYC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4AYC from S2C, [Save to disk]
  • Re-refined 4ayc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4AYC in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4AYC
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4AYC, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ayc_A] [4ayc] [4ayc_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4AYC: [RING ] by SMART
  • Other resources with information on 4AYC
  • Community annotation for 4AYC at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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